Journal article

ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data

Jane Hawkey, Mohammad Hamidian, Ryan R Wick, David J Edwards, Helen Billman-Jacobe, Ruth M Hall, Kathryn E Holt

bioRxiv | Cold Spring Harbor Laboratory

Abstract

Background Insertion sequences (IS) are small transposable elements, commonly found in bacterial genomes. Identifying the location of IS in bacterial genomes can be useful for a variety of purposes including epidemiological tracking and predicting antibiotic resistance. However IS are commonly present in multiple copies in a single genome, which complicates genome assembly and the identification of IS insertion sites. Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, direct from paired-end short read data. Results ISMapper was validated using three types of short read data: (i) simulated reads from a variety o..

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